A good example of thematic magic in disparate subsystems is sanity in CoC. Another is found in the thought-worm micro-process in ED. On in the Bushido RPG. Auto-fail on 1 in the 5th ed combat process. Scattered across TTRPGs are processes that through adroit fusing of theme and method, deliver feel.
CoC Sanity is still run exactly like a skill check. There are additional/different rules around it in terms of the 'sanity subsystem', yes, but it still utilizes a good bit of the %-based BRP mechanical framework. OTOH, weirdly it might have been better built around the ability score part of BRP, since there are few cases where you would make a check against it. My feeling was always that BRP/CoC missed a march effectively by not using %-based ability scores too! That model worked fairly well in Boot Hill, amongst a few other early games which used it (though Boot Hill itself does NOT follow it up with a %-based skill system, which is the next logical step).
Bushido is as crazy as early D&D, and frankly a much worse design overall. It WAS a very thematically focused game, in terms of its outcomes, but I'm not in any way convinced that it was good design. We played quite a bit of it back in the 70's with a guy who was rather an "all things Japanese" freak. He did a good job of GMing it, but the rules were so abysmally complex that we all just took his word for it on all mechanical questions. Having reread it a few years ago I was rather astounded at how completely wacky the rules are... Honestly I doubt anyone who wasn't deeply enthusiastic about the source material could make it work.
I'm not sure what 5e auto fail on a 1 accomplishes exactly. It hardly seems amazingly thematic though. I mean IMHO it gives anyone a small chance of surviving some sure doom (the dragon COULD technically miss you) or of conversely forcing you to account for some slight odds of failure in all cases (you will slip and fall 1 in 20 times, so be ready if you pull enough cat burglaries). I am not really seeing where that is either A) a disparate subsystem (it is just a technical rule of adjudication of checks) nor B) particularly thematic in 5e play.
DW is an interesting case because encapsulated in moves are micro-processes, which so far as I can tell are intentionally not limited in structure. There are process patterns (hold, forward, pick X of Y, etc), albeit these are not intended to be limiting. In a way, DW draws on the OOD pattern crystallised in MtG. Moving forward from there, I have thoughts in the direction of apis or microservices.
As a strawman, I might prefer something like
- tempo - nested clocks (here speaking of costs as much as time: quantums)
- multiple process-spaces, that properly interface
- any number of objects within each process-space, prototyped according to the rules internal to that space
In such a schema, it doesn't matter if an object inside one process-space would be unintelligible from the point of view of another process-space, but objects also can't freely migrate. Tempo rules them all, and is
essential for bite. You can put tempo inside each process-space: it is powerful to also arc it over them.
OK, but how do you apply an effect over the whole space? Suppose I drink a 'potion of speed'? What is the implication within all these different subsystems? They need some common inputs in order to process that, or it needs to act as a 'wrapper' on each and every one of them, accepting their outputs and altering them on accord of this additional factor. If I move, the movement subsystem has to deal with my increased tempo of movement. The combat system needs to account for it too. The healing and initiate systems, etc. (assuming they exist).
Since PbtA is very flat, it has no issue here. You can simply apply something like hold or forward, or even pick X of Y, whichever seems thematically most appropriate to a 'potion of speed'. Perhaps all it does is alter the valence of various elements of fictional positioning (IE the GM will take into account that I move twice as fast as everyone else when adjudicating what moves are made, when, and how). PbtA though is a particular type of system, which I would call 'loosely connected' in that process and principles of play are sort of the 'pudding' and the mechanics are sort of like raisins that float in it. When you invoke a move, the process is very fixed and regularized, but there's a lot that happens 'in the middle' that is subject to a less rigid, though equally principled, process.
4e would, in some respects, be a better guinea pig (one reason I chose it to base my game on, the other just being I like a lot of its flavor). A 'potion of speed' in 4e is pretty darn simple. It gives a +2 power bonus to speed. Speed can feed into movement and possibly a few other things. It could extend that power bonus to other things as well, like initiative, DEX based checks and attacks, etc. (I assume this is not done in 4e because of a concern over the potency of those bonuses vs the availability of the potion). I think this is actually showing how many factors can interact in ways that can be hard to predict. One might consider the possibility that the PbtA style of 'raisins in a cookie' might actually be the most robust, noting that it requires a very simple core design too!